status check missing from multiQC report

0

Entering edit mode

3.1 years ago

Lauren • 0

Hi there,

I have ran multiQC using the following command using the fastQC.zip files

multiqc .

The html file does not contain a heatmap with the FastQC status check? how do I generate this plot in the html report?

thank you,

Lauren

RNA-Seq fastqc • 1.1k views

ADD COMMENT • link 3.1 years ago by Lauren • 0

2

Entering edit mode

multi is not the command for multiqc. It's multiqc. Do you have any aliases in place?

ADD REPLY • link 3.1 years ago by Ram 43k

0

Entering edit mode

sorry that was a typo on there, I entered the command correctly when using multiQC. but I didn't get the heatmap of the status checks as I expected

ADD REPLY • link 3.1 years ago by Lauren • 0

0

Entering edit mode

Did you get any output at all? What did the command line say?

ADD REPLY • link 3.1 years ago by Ram 43k

0

Entering edit mode

What is FastQC status check?

ADD REPLY • link 3.1 years ago by GenoMax 142k

0

Entering edit mode

"Status Checks
Status for each FastQC section showing whether results seem entirely normal (green), slightly abnormal (orange) or very unusual (red)."

ADD REPLY • link 3.1 years ago by Lauren • 0

0

Entering edit mode

How did you install MultiQC? Using conda? Sounds like you may be missing some libraries or something.

ADD REPLY • link 3.1 years ago by GenoMax 142k

0

Entering edit mode

yes I installed via Conda

ADD REPLY • link 3.1 years ago by Lauren • 0

0

Entering edit mode

Do you have all .zip files from FastQC in same dir? FastQC module looks for files that end in _fastqc.zip.

ADD REPLY • link 3.1 years ago by GenoMax 142k

Login before adding your answer.